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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ), 'gf_id' => 'HOM05D001306', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001306' ), 'data_identifier' => 'HOM05D001306', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001306', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '481', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18250' => 'bna', 'A01p21530' => 'bna', 'A01p34220' => 'bna', 'A01p37410' => 'bna', 'A03p41830' => 'bna', 'A05p28260' => 'bna', 'A06p38460' => 'bna', 'A07p12140' => 'bna', 'A08p20530' => 'bna', 'A09p04760' => 'bna', 'Aa31LG10G6060' => 'aar', 'Aa31LG11G8160' => 'aar', 'Aa31LG3G10700' => 'aar', 'Aa31LG8G3940' => 'aar', 'Aa31LG8G7390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2436' => 'aag', 'Actinidia10715' => 'ach', 'Actinidia13372' => 'ach', 'Actinidia14266' => 'ach', 'Actinidia21017' => 'ach', 'Actinidia25830' => 'ach', 'Actinidia35325' => 'ach', 'Ah.04g155030' => 'amhyb', 'Ah.04g155040' => 'amhyb', 'Ah.04g155050' => 'amhyb', 'Ah.04g165570' => 'amhyb', 'AL3G29830' => 'aly', 'AL3G34440' => 'aly', 'AL7G25690' => 'aly', 'AL7G39050' => 'aly', 'AL8G22880' => 'aly', 'Aqoxy2G02845' => 'aox', 'Aqoxy3G01005' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10N228' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DU9TAP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EJE3BD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LY0G2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6049K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PA1P6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QC4UQW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6EXVQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VA5NBW' => 'arhy', 'AT3G16860' => 'ath', 'AT3G20580' => 'ath', 'AT4G16120' => 'ath', 'AT4G27110' => 'ath', 'AT5G49270' => 'ath', 'ATR0706G117' => 'atr', 'ATR0743G153' => 'atr', 'Atru.chr2.3230' => 'acertr', 'Atru.chr4.2942' => 'acertr', 'Atru.chr4.2943' => 'acertr', 'Atru.chr5.1071' => 'acertr', 'AUR62008734' => 'cqu', 'AUR62015669' => 'cqu', 'AUR62016154' => 'cqu', 'AUR62020534' => 'cqu', 'AUR62025503' => 'cqu', 'AUR62035069' => 'cqu', 'BcaB03g12528' => 'bca', 'BcaB04g19116' => 'bca', 'BcaB04g19601' => 'bca', 'BcaB04g20644' => 'bca', 'BcaB04g20871' => 'bca', 'BcaB06g26123' => 'bca', 'BcaC01g03547' => 'bca', 'BcaC03g17589' => 'bca', 'BcaC04g19370' => 'bca', 'BcaC04g23746' => 'bca', 'BcaC05g28312' => 'bca', 'BcaC05g28313' => 'bca', 'BcaC07g38265' => 'bca', 'BcaC07g38272' => 'bca', 'BcaC09g49002' => 'bca', 'BcaC09g50297' => 'bca', 'BcaC09g50616' => 'bca', 'BcaC09g50967' => 'bca', 'BcaNung00227' => 'bca', 'BcaNung03059' => 'bca', 'BcaNung06140' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01080' => 'bna', 'BolC1t01793H' => 'bol', 'BolC1t02258H' => 'bol', 'BolC1t02633H' => 'bol', 'BolC1t04322H' => 'bol', 'BolC1t04702H' => 'bol', 'BolC3t17411H' => 'bol', 'BolC5t31903H' => 'bol', 'BolC5t33089H' => 'bol', 'BolC5t33090H' => 'bol', 'BolC8t48690H' => 'bol', 'BolC8t48698H' => 'bol', 'BolC9t53438H' => 'bol', 'BraA01t01780Z' => 'bra', 'BraA01t02060Z' => 'bra', 'BraA01t03522Z' => 'bra', 'BraA01t03797Z' => 'bra', 'BraA03t13336Z' => 'bra', 'BraA05t21708Z' => 'bra', 'BraA06t26760Z' => 'bra', 'BraA07t28999Z' => 'bra', 'BraA08t34009Z' => 'bra', 'BraA09t36112Z' => 'bra', 'C01p18650' => 'bna', 'C01p23250' => 'bna', 'C01p26880' => 'bna', 'C01p43610' => 'bna', 'C01p47320' => 'bna', 'C02p25870' => 'bna', 'C03p51210' => 'bna', 'C05p31770' => 'bna', 'C05p43730' => 'bna', 'C05p43740' => 'bna', 'C08p10110' => 'bna', 'C08p10190' => 'bna', 'C09p05160' => 'bna', 'C09p56450' => 'bna', 'CAN.G1110.5' => 'can', 'CAN.G121.7' => 'can', 'CAN.G14.3' => 'can', 'CAN.G337.96' => 'can', 'CAN.G569.28' => 'can', 'CAN.G668.34' => 'can', 'CANSAT11G2665' => 'cansat', 'CANSAT25G3029' => 'cansat', 'CANSAT78G0259' => 'cansat', 'CARHR092130' => 'chi', 'CARHR096370' => 'chi', 'CARHR182330' => 'chi', 'CARHR182350' => 'chi', 'CARHR182370' => 'chi', 'CARHR234760' => 'chi', 'CARHR290750' => 'chi', 'Carub.0003s1658' => 'cru', 'Carub.0003s2056' => 'cru', 'Carub.0007s1373' => 'cru', 'Carub.0007s2549' => 'cru', 'Carub.0008s0909' => 'cru', 'Ca_01739_v3' => 'car', 'Ca_21461_v3' => 'car', 'Ca_24371_v3' => 'car', 'Ca_24377_v3' => 'car', 'CBR_g21144' => 'cbr', 'CBR_g22012' => 'cbr', 'CBR_g23547' => 'cbr', 'CBR_g55371' => 'cbr', 'Cc02_g11570' => 'ccan', 'Cc03_g01220' => 'ccan', 'Cc05_g13340' => 'ccan', 'Cc11_g06280' => 'ccan', 'Cc11_g08960' => 'ccan', 'CDE02G2465' => 'cde', 'CDE05G0226' => 'cde', 'CDE12G0724' => 'cde', 'Cfa000262' => 'cfa', 'Cfa015473' => 'cfa', 'Cfa020403' => 'cfa', 'Ciclev10004519m.g' => 'ccl', 'Ciclev10010479m.g' => 'ccl', 'Ciclev10017755m.g' => 'ccl', 'Ciclev10024041m.g' => 'ccl', 'CiPaw.01G142800' => 'cil', 'CiPaw.02G077600' => 'cil', 'CiPaw.09G088300' => 'cil', 'CiPaw.11G185000' => 'cil', 'ClCG05G006360' => 'cla', 'ClCG05G014650' => 'cla', 'ClCG10G005640' => 'cla', 'COL.COLO4_09588' => 'col', 'COL.COLO4_23287' => 'col', 'COL.COLO4_34680' => 'col', 'Cpa.g.sc151.44' => 'cpa', 'Cpa.g.sc9.104' => 'cpa', 'Cpa.g.sc97.52' => 'cpa', 'CsaV3_3G005330' => 'csa', 'CsaV3_3G014980' => 'csa', 'CsaV3_3G023180' => 'csa', 'CsaV3_UNG102760' => 'csa', 'CsaV3_UNG102770' => 'csa', 'CSS0000168' => 'camsi', 'CSS0006294' => 'camsi', 'CSS0023733' => 'camsi', 'CSS0027774' => 'camsi', 'CSS0035693' => 'camsi', 'CSS0041480' => 'camsi', 'DCAR_010026' => 'dca', 'DCAR_018303' => 'dca', 'DCAR_028167' => 'dca', 'DCAR_030488' => 'dca', 'Dinv02066' => 'din', 'Dinv02067' => 'din', 'Dinv10050' => 'din', 'Dinv10053' => 'din', 'Dinv22294' => 'din', 'Dinv40722' => 'din', 'Duzib133G1512' => 'dzi', 'Duzib151G0513' => 'dzi', 'Duzib212G1052' => 'dzi', 'Duzib213G0807' => 'dzi', 'Duzib235G1383' => 'dzi', 'Duzib268G1798' => 'dzi', 'ECA236G0954' => 'eca', 'ECA236G2578' => 'eca', 'ECA246G3972' => 'eca', 'ECA248G0373' => 'eca', 'EL10Ac3g04930' => 'bvu', 'EL10Ac4g07939' => 'bvu', 'EL10Ac7g17593' => 'bvu', 'Eucgr.A00190' => 'egr', 'Eucgr.E04110' => 'egr', 'Eucgr.F03435' => 'egr', 'Eucgr.H04021' => 'egr', 'FAN07G1672' => 'fan', 'FAN11G1019' => 'fan', 'FAN12G0783' => 'fan', 'FAN12G3896' => 'fan', 'FAN16G0703' => 'fan', 'FAN21G0897' => 'fan', 'FAN21G2534' => 'fan', 'FAN25G0282' => 'fan', 'FAN25G2396' => 'fan', 'FvH4_3g02530' => 'fve', 'FvH4_3g21960' => 'fve', 'FvH4_4g19240' => 'fve', 'Glyma.01G240166' => 'gma', 'Glyma.01G240232' => 'gma', 'Glyma.07G243200' => 'gma', 'Glyma.09G039900' => 'gma', 'Glyma.11G003300' => 'gma', 'Glyma.12G213400' => 'gma', 'Glyma.13G288300' => 'gma', 'Glyma.17G030700' => 'gma', 'Gohir.A01G075800' => 'ghi', 'Gohir.A02G052900' => 'ghi', 'Gohir.A06G146100' => 'ghi', 'Gohir.A07G131400' => 'ghi', 'Gohir.A10G169100' => 'ghi', 'Gohir.A11G112200' => 'ghi', 'Gohir.A11G219666' => 'ghi', 'Gohir.A11G243100' => 'ghi', 'Gohir.A13G140700' => 'ghi', 'Gohir.D01G063100' => 'ghi', 'Gohir.D02G057700' => 'ghi', 'Gohir.D06G152300' => 'ghi', 'Gohir.D10G175400' => 'ghi', 'Gohir.D11G117300' => 'ghi', 'Gohir.D13G145500' => 'ghi', 'Gorai.002G083800' => 'gra', 'Gorai.005G065200' => 'gra', 'Gorai.007G125700' => 'gra', 'Gorai.010G177700' => 'gra', 'Gorai.011G196300' => 'gra', 'Gorai.013G163300' => 'gra', 'GSVIVG01001979001' => 'vvi', 'GSVIVG01012641001' => 'vvi', 'GSVIVG01028070001' => 'vvi', 'GSVIVG01035050001' => 'vvi', 'HanXRQChr01g0030171' => 'han', 'HanXRQChr11g0337841' => 'han', 'HanXRQChr16g0511271' => 'han', 'Haze_01098' => 'cav', 'Haze_01099' => 'cav', 'Haze_06753' => 'cav', 'Haze_06761' => 'cav', 'Haze_09630' => 'cav', 'Hma1.2p1_0013F.1_g008990' => 'hma', 'Hma1.2p1_0212F.1_g090190' => 'hma', 'Hma1.2p1_1564F.1_g290910' => 'hma', 'Hma1.2p1_1564F.1_g290920' => 'hma', 'HPP92_006900' => 'vpl', 'HPP92_010098' => 'vpl', 'HPP92_010099' => 'vpl', 'HPP92_025193' => 'vpl', 'Hund11949' => 'sun', 'Lalb_Chr05g0210871' => 'lal', 'Lalb_Chr07g0182201' => 'lal', 'Lalb_Chr13g0298301' => 'lal', 'Lalb_Chr14g0366201' => 'lal', 'Lalb_Chr24g0400261' => 'lal', 'Lj1A866T45' => 'lonja', 'Lj1g0016674' => 'lja', 'Lj2A1201T50' => 'lonja', 'Lj3g0008984' => 'lja', 'Lj4g0012791' => 'lja', 'Lj5P360T6' => 'lonja', 'Lj5P400T24' => 'lonja', 'Lj6A684T56' => 'lonja', 'Lj6g0008237' => 'lja', 'Lj8A166T90' => 'lonja', 'Lsat_1_v5_gn_1_44200' => 'lsa', 'Lsat_1_v5_gn_5_115340' => 'lsa', 'Lsat_1_v5_gn_6_115101' => 'lsa', 'Lsat_1_v5_gn_7_109521' => 'lsa', 'Lsat_1_v5_gn_8_165141' => 'lsa', 'Manes.01G223900' => 'mes', 'Manes.03G201100' => 'mes', 'Manes.15G007300' => 'mes', 'Manes.17G036300' => 'mes', 'Mapoly0001s0100' => 'mpo', 'Mapoly0001s0227' => 'mpo', 'MBI18_g05906_MAGBIO' => 'mbi', 'MBI18_g27946_MAGBIO' => 'mbi', 'MD03G1209900' => 'mdo', 'MD10G1315500' => 'mdo', 'MD11G1224600' => 'mdo', 'MD13G1159500' => 'mdo', 'MD13G1159600' => 'mdo', 'MD16G1159300' => 'mdo', 'Medtr2g034950' => 'mtr', 'Medtr2g083210' => 'mtr', 'Medtr4g121060' => 'mtr', 'Medtr4g121080' => 'mtr', 'Medtr5g005590' => 'mtr', 'MELO3C006694.2' => 'cme', 'MELO3C018094.2' => 'cme', 'MELO3C025407.2' => 'cme', 'Migut.D00115' => 'egut', 'Migut.G00110' => 'egut', 'Migut.M01800' => 'egut', 'MSTRG.10127' => 'ama', 'MSTRG.14421' => 'ama', 'MSTRG.3876' => 'ama', 'MSTRG.6895' => 'ama', 'Nitab4.5_0000080g0300' => 'nta', 'Nitab4.5_0000116g0190' => 'nta', 'Nitab4.5_0000616g0070' => 'nta', 'Nitab4.5_0000629g0010' => 'nta', 'Nitab4.5_0002229g0150' => 'nta', 'Nitab4.5_0002342g0060' => 'nta', 'Nitab4.5_0002347g0030' => 'nta', 'Nitab4.5_0002454g0030' => 'nta', 'Nitab4.5_0008018g0010' => 'nta', 'Nitab4.5_0008369g0010' => 'nta', 'Nitab4.5_0013434g0010' => 'nta', 'Nn1g03609' => 'nnu', 'Nn1g07059' => 'nnu', 'Nn3g21598' => 'nnu', 'Nn4g25686' => 'nnu', 'Oeu006435.1' => 'oeu', 'Oeu042918.1' => 'oeu', 'Oeu061712.1' => 'oeu', 'Oeu062609.1' => 'oeu', 'Os03g0301200' => 'osa', 'Os06g0685100' => 'osa', 'Os07g0690900' => 'osa', 'Peaxi162Scf00001g03114' => 'pax', 'Peaxi162Scf00065g00041' => 'pax', 'Peaxi162Scf00262g00012' => 'pax', 'Peaxi162Scf00407g00039' => 'pax', 'Peaxi162Scf00450g00875' => 'pax', 'PGR004G1546' => 'pgr', 'PGR031G3293' => 'pgr', 'PGR031G3527' => 'pgr', 'PGR044G1002' => 'pgr', 'PGSC0003DMG400001032' => 'stu', 'PGSC0003DMG400001036' => 'stu', 'PGSC0003DMG400002075' => 'stu', 'PGSC0003DMG400014428' => 'stu', 'PGSC0003DMG400025627' => 'stu', 'PGSC0003DMG402025624' => 'stu', 'Phvul.002G048300' => 'pvu', 'Phvul.003G110200' => 'pvu', 'Phvul.005G092500' => 'pvu', 'Phvul.009G253300' => 'pvu', 'Potri.001G419000' => 'ptr', 'Potri.010G001100' => 'ptr', 'Potri.011G135200' => 'ptr', 'Potri.014G125300' => 'ptr', 'Pp3c14_12030' => 'ppa', 'Pp3c17_6920' => 'ppa', 'Pp3c1_25450' => 'ppa', 'Pp3c25_1920' => 'ppa', 'Pp3c27_3700' => 'ppa', 'Pp3c2_18020' => 'ppa', 'Pp3c4_14561' => 'ppa', 'Pp3c5_11390' => 'ppa', 'Pp3c6_14710' => 'ppa', 'Pp3c6_14750' => 'ppa', 'Prupe.1G126300' => 'ppe', 'Prupe.4G025000' => 'ppe', 'Prupe.4G205300' => 'ppe', 'Psat0s1646g0120' => 'psa', 'Psat1g158040' => 'psa', 'Psat4g224680' => 'psa', 'Psat5g252040' => 'psa', 'PSO017G4897' => 'pso', 'PSO063G2258' => 'pso', 'PSO063G4991' => 'pso', 'PSO541G0395' => 'pso', 'PSO675G3114' => 'pso', 'QL05p074693' => 'qlo', 'QL06p011206' => 'qlo', 'QL08p012745' => 'qlo', 'QL08p012872' => 'qlo', 'RcHm_v2.0_Chr4g0424221' => 'rch', 'RcHm_v2.0_Chr5g0003851' => 'rch', 'RcHm_v2.0_Chr5g0037811' => 'rch', 'Rhsim02G0006000' => 'rsi', 'RhsimUnG0252700' => 'rsi', 'Sabra10G0000900' => 'sbr', 'Sabra14G0093100' => 'sbr', 'Sabra16G0284500' => 'sbr', 'SalBow1G3776' => 'sbo', 'SalBow1G4392' => 'sbo', 'SalBow8G2811' => 'sbo', 'SalBow8G2951' => 'sbo', 'SalBow8G5110' => 'sbo', 'Sc03g0008880' => 'sci', 'Sc19g0003430' => 'sci', 'Sc25g0003480' => 'sci', 'Sed0008922' => 'sed', 'Sed0018984' => 'sed', 'Sed0027502' => 'sed', 'SEGI_31974' => 'sgi', 'SGA_v2.0_scaffold100G29636' => 'sas', 'SGA_v2.0_scaffold120G32896' => 'sas', 'SGA_v2.0_scaffold1211G53864' => 'sas', 'SGA_v2.0_scaffold22G09783' => 'sas', 'SGA_v2.0_scaffold444G51718' => 'sas', 'SHI00187' => 'shi', 'SHI31834' => 'shi', 'SMO334G0090' => 'smo', 'Solyc01g065530.3' => 'sly', 'Solyc02g080240.2' => 'sly', 'Solyc07g064200.4' => 'sly', 'Solyc09g075540.1' => 'sly', 'Solyc10g006450.3' => 'sly', 'Sopen01g026870' => 'spe', 'Sopen02g024960' => 'spe', 'Sopen07g032340' => 'spe', 'Sopen09g030330' => 'spe', 'Sopen10g002400' => 'spe', 'Sp2g19630' => 'spa', 'Sp3g15110' => 'spa', 'Sp3g18600' => 'spa', 'Sp7g14580' => 'spa', 'Sp7g25080' => 'spa', 'TAR365G0497' => 'tar', 'TAR624G0946' => 'tar', 'TAR626G1340' => 'tar', 'TAR627G0007' => 'tar', 'TAR633G1804' => 'tar', 'THA.LOC104798780' => 'tha', 'THA.LOC104802596' => 'tha', 'THA.LOC104812530' => 'tha', 'THA.LOC104816922' => 'tha', 'THA.LOC104821789' => 'tha', 'THA.LOC104827084' => 'tha', 'Thecc.01G307800' => 'tca', 'Thecc.04G294100' => 'tca', 'Thecc.06G215500' => 'tca', 'Thecc.07G050500' => 'tca', 'Thhalv10003778m.g' => 'esa', 'Thhalv10020212m.g' => 'esa', 'Thhalv10020239m.g' => 'esa', 'Thhalv10024619m.g' => 'esa', 'Thhalv10024623m.g' => 'esa', 'TPR.G16829' => 'tpr', 'TPR.G19999' => 'tpr', 'TPR.G27942' => 'tpr', 'TPR.G39899' => 'tpr', 'TPR.G8304' => 'tpr', 'TWI09G0100' => 'twi', 'TWI36G0831' => 'twi', 'TWI38G0358' => 'twi', 'TWI38G1418' => 'twi', 'TWI39G0978' => 'twi', 'TWI63G0615' => 'twi', 'TWI73G0196' => 'twi', 'unitig_0.g1055' => 'ugi', 'unitig_37.g12404' => 'ugi', 'vmacro09743' => 'vma', 'vmacro15200' => 'vma', 'VMungo0720G1106' => 'vmu', 'VMungo1080G1083' => 'vmu', 'VMungo1215G1410' => 'vmu', 'VMungo1215G1932' => 'vmu', 'VMungo1215G3021' => 'vmu', 'VMungo1309G2973' => 'vmu', 'Zm00001eb014120' => 'zma', 'Zm00001eb323040' => 'zma' ) $gf_id = 'HOM05D001306' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001306' ) $data_identifier = 'HOM05D001306' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 21, 'bol' => (int) 12, 'bra' => (int) 10, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 10, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 6, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb323040' $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